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Expand Up @@ -30,7 +30,7 @@ While this section may be used as an entry point, learning about genomic analyse

1. __Install R__
Instructions on how to install R can be found at the [R homepage](https://www.r-project.org/).
Please make sure you have the most current version of R (3.4.4, Someone to lean on).
Please make sure you have the most current version of R (at least 3.4.4, Someone to lean on).
2. __Install RStudio__
Instructions on how to install the RStudio integrated development environment (IDE) can be found at the [RStudio download site](https://www.rstudio.com/products/rstudio/download/).
Choose the 'RStudio Desktop Open Source License' (free) version.
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131 changes: 79 additions & 52 deletions workshop.html
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Expand Down Expand Up @@ -395,13 +422,13 @@ <h3>ICPP, Boston, Massachusetts, 2018</h3>
<div id="before-you-arrive-please-make-sure-you-install-the-following-required-materials" class="section level2">
<h2>Before you arrive please make sure you install the following required materials</h2>
<ol style="list-style-type: decimal">
<li><strong>Install R</strong> Instructions on how to install R can be found at the <a href="https://www.r-project.org/">R homepage</a>. Please make sure you have the most current version of R (3.4.4, Someone to lean on).</li>
<li><strong>Install R</strong> Instructions on how to install R can be found at the <a href="https://www.r-project.org/">R homepage</a>. Please make sure you have the most current version of R (at least 3.4.4, Someone to lean on).</li>
<li><strong>Install RStudio</strong><br />
Instructions on how to install the RStudio integrated development environment (IDE) can be found at the <a href="https://www.rstudio.com/products/rstudio/download/">RStudio download site</a>. Choose the ‘RStudio Desktop Open Source License’ (free) version.</li>
<li><strong>Install R packages</strong><br />
You can install the R packages we will be using during the workshop by starting R and copying and pasting the below command into the R console.</li>
</ol>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">install.packages</span>(<span class="kw">c</span>(<span class="st">&quot;adegenet&quot;</span>, <span class="st">&quot;ape&quot;</span>, <span class="st">&quot;cowplot&quot;</span>, <span class="st">&quot;devtools&quot;</span>, <span class="st">&quot;dplyr&quot;</span>, <span class="st">&quot;ggplot2&quot;</span>, <span class="st">&quot;hierfstat&quot;</span>, <span class="st">&quot;igraph&quot;</span>, <span class="st">&quot;knitr&quot;</span>, <span class="st">&quot;lattice&quot;</span>, <span class="st">&quot;magrittr&quot;</span>, <span class="st">&quot;mmod&quot;</span>, <span class="st">&quot;pegas&quot;</span>, <span class="st">&quot;pinfsc50&quot;</span>, <span class="st">&quot;poppr&quot;</span>, <span class="st">&quot;RColorBrewer&quot;</span>, <span class="st">&quot;reshape2&quot;</span>, <span class="st">&quot;treemap&quot;</span>, <span class="st">&quot;vcfR&quot;</span>, <span class="st">&quot;vegan&quot;</span>, <span class="st">&quot;viridisLite&quot;</span>))</code></pre></div>
<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="kw">install.packages</span>(<span class="kw">c</span>(<span class="st">&quot;adegenet&quot;</span>, <span class="st">&quot;ape&quot;</span>, <span class="st">&quot;cowplot&quot;</span>, <span class="st">&quot;devtools&quot;</span>, <span class="st">&quot;dplyr&quot;</span>, <span class="st">&quot;ggplot2&quot;</span>, <span class="st">&quot;hierfstat&quot;</span>, <span class="st">&quot;igraph&quot;</span>, <span class="st">&quot;knitr&quot;</span>, <span class="st">&quot;lattice&quot;</span>, <span class="st">&quot;magrittr&quot;</span>, <span class="st">&quot;mmod&quot;</span>, <span class="st">&quot;pegas&quot;</span>, <span class="st">&quot;pinfsc50&quot;</span>, <span class="st">&quot;poppr&quot;</span>, <span class="st">&quot;RColorBrewer&quot;</span>, <span class="st">&quot;reshape2&quot;</span>, <span class="st">&quot;treemap&quot;</span>, <span class="st">&quot;vcfR&quot;</span>, <span class="st">&quot;vegan&quot;</span>, <span class="st">&quot;viridisLite&quot;</span>))</a></code></pre></div>
<ol start="4" style="list-style-type: decimal">
<li><strong>Download the following datasets into a new folder called <code>APS_Workshop/</code>: </strong><br />
When you click on the below links our GitHub site should open in your web browser. Click on the <code>Download</code> button and save each file to your local <code>APS_Workshop/</code> folder.</li>
Expand All @@ -415,12 +442,12 @@ <h2>Before you arrive please make sure you install the following required materi
<li><strong>Test that your system is ready:</strong><br />
You should now be able to validate that the resources you need are ready. Change directory to <code>APS_Workshop</code> and copy and paste the below command into the R console.</li>
</ol>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="cf">if</span>(<span class="kw">require</span>(devtools)){
devtools<span class="op">::</span><span class="kw">source_gist</span>(<span class="st">&quot;01a3d8efb21e0a4dbac0735270d147af&quot;</span>, <span class="dt">filename=</span><span class="st">&quot;apstest.R&quot;</span>)
} <span class="cf">else</span> {
<span class="kw">print</span>(<span class="st">&quot;Please install the package devtools.&quot;</span>)
<span class="kw">print</span>(<span class="st">&quot;Use: install.packages(&#39;devtools&#39;)&quot;</span>)
}</code></pre></div>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="cf">if</span>(<span class="kw">require</span>(devtools)){</a>
<a class="sourceLine" id="cb2-2" data-line-number="2"> devtools<span class="op">::</span><span class="kw">source_gist</span>(<span class="st">&quot;01a3d8efb21e0a4dbac0735270d147af&quot;</span>, <span class="dt">filename=</span><span class="st">&quot;apstest.R&quot;</span>) </a>
<a class="sourceLine" id="cb2-3" data-line-number="3">} <span class="cf">else</span> {</a>
<a class="sourceLine" id="cb2-4" data-line-number="4"> <span class="kw">print</span>(<span class="st">&quot;Please install the package devtools.&quot;</span>)</a>
<a class="sourceLine" id="cb2-5" data-line-number="5"> <span class="kw">print</span>(<span class="st">&quot;Use: install.packages(&#39;devtools&#39;)&quot;</span>)</a>
<a class="sourceLine" id="cb2-6" data-line-number="6">}</a></code></pre></div>
<p>This should output some tests to the console. It should also generate a report file called <code>apstest.txt</code>. The report file should look exactly like <a href="https://github.com/grunwaldlab/Population_Genetics_in_R/blob/master/apstest.txt">this file</a>. If your results are different, and you don’t understand why, send us an email with the report as an attachment.</p>
<ol start="6" style="list-style-type: decimal">
<li><strong>If you have never worked with R, please review the <a href="intro_to_R.html">Introduction to R</a> page</strong></li>
Expand All @@ -429,15 +456,15 @@ <h2>Before you arrive please make sure you install the following required materi
<div id="your-first-homework" class="section level2">
<h2>Your first homework</h2>
<p>Some aspects of analyzing genetic data are rather technical. Others are more stylistic. An example is the presentation of the data. The presentation of data may include choices in color schemes and sometimes the perspective on the data. Below is a little example that you can copy and paste into your R console. Explore how changing the number in <code>set.seed()</code> changes the plot. Remember to execute the <code>plot_poppr_msn(partial_clone, myMsn, palette = brewer.pal(n=4, name = &quot;Set1&quot;))</code> function again. There are other examples that are commented out (i.e., the lines begin with <code>#</code> so they are not executed). Try removing the comment character (<code>#</code>) and see how the different parameters affect the plot. This example should validate that you have successfully installed <code>poppr</code> and hopefully provides a fun example that may inspire you to explore more options.</p>
<div class="sourceCode"><pre class="sourceCode r"><code class="sourceCode r"><span class="kw">library</span>(RColorBrewer)
<span class="kw">library</span>(viridisLite)
<span class="kw">library</span>(poppr)
<span class="kw">data</span>(partial_clone)
myMsn &lt;-<span class="st"> </span><span class="kw">bruvo.msn</span>(partial_clone, <span class="dt">include.ties =</span> <span class="ot">TRUE</span>, <span class="dt">showplot =</span> <span class="ot">FALSE</span>)
<span class="kw">set.seed</span>(<span class="dv">9</span>)
<span class="kw">plot_poppr_msn</span>(partial_clone, myMsn, <span class="dt">palette =</span> <span class="kw">brewer.pal</span>(<span class="dt">n=</span><span class="dv">4</span>, <span class="dt">name =</span> <span class="st">&quot;Set1&quot;</span>))
<span class="co">#plot_poppr_msn(partial_clone, myMsn, palette = magma(n=4, begin = 0.2, end = 0.8))</span>
<span class="co">#plot_poppr_msn(partial_clone, myMsn, palette = plasma(n=4))</span></code></pre></div>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw">library</span>(RColorBrewer)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="kw">library</span>(viridisLite)</a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="kw">library</span>(poppr)</a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="kw">data</span>(partial_clone)</a>
<a class="sourceLine" id="cb3-5" data-line-number="5">myMsn &lt;-<span class="st"> </span><span class="kw">bruvo.msn</span>(partial_clone, <span class="dt">include.ties =</span> <span class="ot">TRUE</span>, <span class="dt">showplot =</span> <span class="ot">FALSE</span>)</a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="kw">set.seed</span>(<span class="dv">9</span>)</a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw">plot_poppr_msn</span>(partial_clone, myMsn, <span class="dt">palette =</span> <span class="kw">brewer.pal</span>(<span class="dt">n=</span><span class="dv">4</span>, <span class="dt">name =</span> <span class="st">&quot;Set1&quot;</span>))</a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co">#plot_poppr_msn(partial_clone, myMsn, palette = magma(n=4, begin = 0.2, end = 0.8))</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co">#plot_poppr_msn(partial_clone, myMsn, palette = plasma(n=4))</span></a></code></pre></div>
</div>
<div id="workshop-agenda" class="section level2">
<h2>Workshop agenda</h2>
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